A threshold-based method cannot capture CNV at clone Chr4tp-6G5. The log2 ratios for all clones on chromosome 4 are plotted for three samples: NA11829 (top), NA12044 (middle) and NA19093 (bottom) on (a) uncorrected and (b) corrected data. The log2 ratios are plotted on the y-axis and the corresponding genomic position of each clone is plotted on the x-axis. The blue spot flags a clone (Chr4tp-6G5) whose CNV status in this individual had previously been determined using a genotyping algorithm . This clone has been classified as a gain in samples NA11829 and NA19093 and a loss in sample NA12044. All of the points with an absolute log ratio greater than 0.05 are highlighted in red. The vertical gray dashed line indicates the position of the centromere. A threshold sensitive enough to identify this clone results in a large number of clones being flagged (Additional data file 5), many of which almost certainly represent false positives due to confounding with the peaks and troughs of the wave.
Marioni et al. Genome Biology 2007 8:R228 doi:10.1186/gb-2007-8-10-r228